Recent work has highlighted the need to account for hierarchical patterns of genetic structure when estimating evolutionary and ecological parameters of interest. This caution is particularly relevant to studies of riverine organisms, where hierarchical structure appears to be commonplace. Here we indirectly estimate dispersal distance in a hierarchically structured freshwater fish, Mogurnda adspersa. Microsatellite and mitochondrial (mtDNA) data were obtained for 443 individuals across 27 sites separated by an average of 1.3 kilometers within creeks of southeastern Queensland, Australia. Significant genetic structure was found among sites (mtDNA ΦST = 0.508; microsatellite FST = 0.225, F′ST = 0.340). Various clustering methods produced congruent patterns of hierarchical structure reflecting stream architecture. Partial mantel tests identified contiguous sets of sample sites where isolation-by-distance (IBD) explained FST variation without significant contribution of hierarchical structure. Analysis of mean natal dispersal distance (σ) within sets of IBD-linked sample sites suggested most dispersal occurs over <1 km and the average effective density (De) was estimated at 11.5 individuals.km-1; indicating sedentary behaviour and small effective population size are responsible for the remarkable patterns of genetic structure observed. Our results demonstrate that Rousset’s regression-based method is applicable to estimating the scale of dispersal in riverine organisms, and that identifying contiguous populations which satisfy the assumptions of this model is achievable with genetic clustering methods and partial correlations.